Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

[Fischl, Bruce R.,PHD]

Have you tried changing the window levels (contrast and brightness)?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Wighton, Paul
Sent: Friday, September 30, 2022 10:17 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

Hi Justina,

I don't know too much about FreeView, unfortunately.  Hopefully others on the 
list have some ideas.

Are you trying to run FreeView inside the FreeSurfer virtual machine?  What 
operating system are you using?

-Paul

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Justina Lee 
mailto:justinale...@gmail.com>>
Sent: Friday, September 30, 2022 5:36 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution
Hi Paul,

Redownloading freesurfer seems to have done the trick, but I still come across 
the issue with loading data and seeing nothing on freeview. Hope you can help 
me with this tiny problem.

Sincerely,
Justina

On Fri, Sep 30, 2022 at 10:10 AM Justina Lee 
mailto:justinale...@gmail.com>> wrote:
Hi Paul,

Thank you for all your help with some technical issues.
I was wondering if you could help me with one tiny issue I have been unable to 
solve, which is the usage of freeview on my computer.
The installation has been completed successfully, but when I try to open any 
data, I seem to not see anything. Upon trying again recently, now opening 
freeview does not seem to work at all. (For example, trying to run the command 
freeview -v T1.mgz does not produce a freeview to open up on another window.)
Could you help me with this? I'm sorry for the troubles once more.

Sincerely,
Justina

On Thu, Sep 15, 2022 at 4:00 PM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
One more note:

The command:
export SUBJECTS_DIR=/home/ylee6/ADIPA_data

May or may not work, depending on the type of shell environment you are using.  
If it doesn't work, you can try:
setenv SUBJECTS_DIR /home/ylee6/ADIPA_data

To set the environment variable

-Paul

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>>
Sent: Thursday, September 15, 2022 9:56 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

Hi Justina,

Ok so on your computer, the subjects are located in /home/ylee6/ADIPA_data, but 
the SUBJECTS_DIR environment variable is set to 
/usr/local/freesurfer/7.3.2/subjects.

There are two ways we can fix this.

1) We can change the SUBJECTS_DIR environment variable and then run 
segmentHA_T1.sh:

export SUBJECTS_DIR=/home/ylee6/ADIPA_data
segmentHA_T1.sh 26

2) Or, we can pass the subjects dir as a parameter to segmentHA_T1.sh, telling 
it to use that directory instead of the environment variable:

segmentHA_T1.sh 26 /home/ylee6/ADIPA_data

You were close with your command "segmentHA_T1.sh 26 
[/usr/local/freesurfer/7.3.2/subjects]"! Just FYI when you see a parameter in 
square brackets ([]) it means the parameter is optional, you shouldn't include 
the brackets when running the command.

Glad I could be helpful,

-Paul

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Justina Lee 
mailto:justinale...@gmail.com>>
Sent: Thursday, September 15, 2022 7:51 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution
Hi Paul,

Thank you for your help tremendously throughout this process.

Firstly, attached you will find the requested recon-all.log for the subject 
26 (originally located in the path /home/ylee6/ADIPA_data/26/scripts), 
in which at the end of the log you can see that the recon-all is completed 
successfully.

Secondly, with the output from the 'env' command you can see it described as 
such below:

SHELL=/bin/bash
WSL_DISTRO_NAME=Ubuntu
OS=Linux
MINC_BIN_DIR=/usr/local/freesurfer/7.3.2/mni/bin
FSFAST_HOME=/usr/local/freesurfer/7.3.2/fsfast
FREESURFER=/usr/local/freesurfer/7.3.2
MNI_DATAPATH=/usr/local/freesurfer/7.3.2/mni/data
FS_OVERRIDE=0
NAME=LAPTOP-63HA9ANS
PWD=/home/ylee6/ADIPA_data/26/mri
LOGNAME=ylee6
FUNCTIONALS_DIR=/usr/local/freesurfer/7.3.2/sessions
MOTD_SHOWN=update-motd
HOME=/home/ylee6
LANG=C.UTF-8
WSL_INTEROP=/run/WSL/8_interop
MINC_LIB_DIR=/usr/local/freesurfer/

Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

[Wighton, Paul]

Hi Justina,

Since this is the VM, one thing to try is to follow along with the instructions 
here
https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription/Remote_Qualify

Particularly the part where 3d acceleration is disabled.  If that doesn't work, 
please start a new thread.

Good luck!

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Justina Lee 

Sent: Friday, September 30, 2022 10:25 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

hi Paul,

yes that’s right, i can ask again in the freesurfer mailing list if someone 
else can help with this. I’m trying to run Freeview inside the Freesurfer 
virtual machine using Ubuntu 20 on the linux windows operating system. It seems 
to be running again but doesn’t show me any images
Thanks for the help!

Sincerely,
Justina

On Fri, Sep 30, 2022 at 4:18 PM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
Hi Justina,

I don't know too much about FreeView, unfortunately.  Hopefully others on the 
list have some ideas.

Are you trying to run FreeView inside the FreeSurfer virtual machine?  What 
operating system are you using?

-Paul

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Justina Lee 
mailto:justinale...@gmail.com>>
Sent: Friday, September 30, 2022 5:36 AM

To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Hi Paul,

Redownloading freesurfer seems to have done the trick, but I still come across 
the issue with loading data and seeing nothing on freeview. Hope you can help 
me with this tiny problem.

Sincerely,
Justina

On Fri, Sep 30, 2022 at 10:10 AM Justina Lee 
mailto:justinale...@gmail.com>> wrote:
Hi Paul,

Thank you for all your help with some technical issues.
I was wondering if you could help me with one tiny issue I have been unable to 
solve, which is the usage of freeview on my computer.
The installation has been completed successfully, but when I try to open any 
data, I seem to not see anything. Upon trying again recently, now opening 
freeview does not seem to work at all. (For example, trying to run the command 
freeview -v T1.mgz does not produce a freeview to open up on another window.)
Could you help me with this? I'm sorry for the troubles once more.

Sincerely,
Justina

On Thu, Sep 15, 2022 at 4:00 PM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
One more note:

The command:
export SUBJECTS_DIR=/home/ylee6/ADIPA_data

May or may not work, depending on the type of shell environment you are using.  
If it doesn't work, you can try:
setenv SUBJECTS_DIR /home/ylee6/ADIPA_data

To set the environment variable

-Paul

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>>
Sent: Thursday, September 15, 2022 9:56 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

Hi Justina,

Ok so on your computer, the subjects are located in /home/ylee6/ADIPA_data, but 
the SUBJECTS_DIR environment variable is set to 
/usr/local/freesurfer/7.3.2/subjects.

There are two ways we can fix this.

1) We can change the SUBJECTS_DIR environment variable and then run 
segmentHA_T1.sh:

export SUBJECTS_DIR=/home/ylee6/ADIPA_data
segmentHA_T1.sh 26

2) Or, we can pass the subjects dir as a parameter to segmentHA_T1.sh, telling 
it to use that directory instead of the environment variable:

segmentHA_T1.sh 26 /home/ylee6/ADIPA_data

You were close with your command "segmentHA_T1.sh 26 
[/usr/local/freesurfer/7.3.2/subjects]"! Just FYI when you see a parameter in 
square brackets ([]) it means the parameter is optional, you shouldn't include 
the brackets when running the command.

Glad I could be helpful,

-Paul

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Justina Lee 
mailto:justinale...@gmail.com>>
Sent: Thursday, September 15, 2022 7:51 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Hi Paul,

Thank you for your help tremendously throughout this process.

Firstly, attached you will find the requested recon-all.log for the subject 
26 (originally loc

Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

[Wighton, Paul]

Hi Justina,

I don't know too much about FreeView, unfortunately.  Hopefully others on the 
list have some ideas.

Are you trying to run FreeView inside the FreeSurfer virtual machine?  What 
operating system are you using?

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Justina Lee 

Sent: Friday, September 30, 2022 5:36 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Hi Paul,

Redownloading freesurfer seems to have done the trick, but I still come across 
the issue with loading data and seeing nothing on freeview. Hope you can help 
me with this tiny problem.

Sincerely,
Justina

On Fri, Sep 30, 2022 at 10:10 AM Justina Lee 
mailto:justinale...@gmail.com>> wrote:
Hi Paul,

Thank you for all your help with some technical issues.
I was wondering if you could help me with one tiny issue I have been unable to 
solve, which is the usage of freeview on my computer.
The installation has been completed successfully, but when I try to open any 
data, I seem to not see anything. Upon trying again recently, now opening 
freeview does not seem to work at all. (For example, trying to run the command 
freeview -v T1.mgz does not produce a freeview to open up on another window.)
Could you help me with this? I'm sorry for the troubles once more.

Sincerely,
Justina

On Thu, Sep 15, 2022 at 4:00 PM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
One more note:

The command:
export SUBJECTS_DIR=/home/ylee6/ADIPA_data

May or may not work, depending on the type of shell environment you are using.  
If it doesn't work, you can try:
setenv SUBJECTS_DIR /home/ylee6/ADIPA_data

To set the environment variable

-Paul

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>>
Sent: Thursday, September 15, 2022 9:56 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

Hi Justina,

Ok so on your computer, the subjects are located in /home/ylee6/ADIPA_data, but 
the SUBJECTS_DIR environment variable is set to 
/usr/local/freesurfer/7.3.2/subjects.

There are two ways we can fix this.

1) We can change the SUBJECTS_DIR environment variable and then run 
segmentHA_T1.sh:

export SUBJECTS_DIR=/home/ylee6/ADIPA_data
segmentHA_T1.sh 26

2) Or, we can pass the subjects dir as a parameter to segmentHA_T1.sh, telling 
it to use that directory instead of the environment variable:

segmentHA_T1.sh 26 /home/ylee6/ADIPA_data

You were close with your command "segmentHA_T1.sh 26 
[/usr/local/freesurfer/7.3.2/subjects]"! Just FYI when you see a parameter in 
square brackets ([]) it means the parameter is optional, you shouldn't include 
the brackets when running the command.

Glad I could be helpful,

-Paul

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Justina Lee 
mailto:justinale...@gmail.com>>
Sent: Thursday, September 15, 2022 7:51 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Hi Paul,

Thank you for your help tremendously throughout this process.

Firstly, attached you will find the requested recon-all.log for the subject 
26 (originally located in the path /home/ylee6/ADIPA_data/26/scripts), 
in which at the end of the log you can see that the recon-all is completed 
successfully.

Secondly, with the output from the 'env' command you can see it described as 
such below:

SHELL=/bin/bash
WSL_DISTRO_NAME=Ubuntu
OS=Linux
MINC_BIN_DIR=/usr/local/freesurfer/7.3.2/mni/bin
FSFAST_HOME=/usr/local/freesurfer/7.3.2/fsfast
FREESURFER=/usr/local/freesurfer/7.3.2
MNI_DATAPATH=/usr/local/freesurfer/7.3.2/mni/data
FS_OVERRIDE=0
NAME=LAPTOP-63HA9ANS
PWD=/home/ylee6/ADIPA_data/26/mri
LOGNAME=ylee6
FUNCTIONALS_DIR=/usr/local/freesurfer/7.3.2/sessions
MOTD_SHOWN=update-motd
HOME=/home/ylee6
LANG=C.UTF-8
WSL_INTEROP=/run/WSL/8_interop
MINC_LIB_DIR=/usr/local/freesurfer/7.3.2/mni/lib
LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=0

Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

[Justina Lee]

External Email - Use Caution

Hi Paul,

Redownloading freesurfer seems to have done the trick, but I still come
across the issue with loading data and seeing nothing on freeview. Hope you
can help me with this tiny problem.

Sincerely,
Justina

On Fri, Sep 30, 2022 at 10:10 AM Justina Lee  wrote:

> Hi Paul,
>
> Thank you for all your help with some technical issues.
> I was wondering if you could help me with one tiny issue I have been
> unable to solve, which is the usage of freeview on my computer.
> The installation has been completed successfully, but when I try to open
> any data, I seem to not see anything. Upon trying again recently, now
> opening freeview does not seem to work at all. (For example, trying to run
> the command freeview -v T1.mgz does not produce a freeview to open up on
> another window.)
> Could you help me with this? I'm sorry for the troubles once more.
>
> Sincerely,
> Justina
>
> On Thu, Sep 15, 2022 at 4:00 PM Wighton, Paul 
> wrote:
>
>> One more note:
>>
>> The command:
>> export SUBJECTS_DIR=/home/ylee6/ADIPA_data
>>
>> May or may not work, depending on the type of shell environment you are
>> using.  If it doesn't work, you can try:
>> setenv SUBJECTS_DIR /home/ylee6/ADIPA_data
>>
>> To set the environment variable
>>
>> -Paul
>> --
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Wighton, Paul <
>> pwigh...@mgh.harvard.edu>
>> *Sent:* Thursday, September 15, 2022 9:56 AM
>> *To:* Freesurfer support list 
>> *Subject:* Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command
>> not found
>>
>> Hi Justina,
>>
>> Ok so on your computer, the subjects are located in
>> /home/ylee6/ADIPA_data, but the SUBJECTS_DIR environment variable is set to
>> /usr/local/freesurfer/7.3.2/subjects.
>>
>> There are two ways we can fix this.
>>
>> 1) We can change the SUBJECTS_DIR environment variable and then run
>> segmentHA_T1.sh:
>>
>> export SUBJECTS_DIR=/home/ylee6/ADIPA_data
>> segmentHA_T1.sh 26
>>
>> 2) Or, we can pass the subjects dir as a parameter to segmentHA_T1.sh,
>> telling it to use that directory instead of the environment variable:
>>
>> segmentHA_T1.sh 26 /home/ylee6/ADIPA_data
>>
>> You were close with your command "segmentHA_T1.sh 26
>> [/usr/local/freesurfer/7.3.2/subjects]"! Just FYI when you see a parameter
>> in square brackets ([]) it means the parameter is optional, you shouldn't
>> include the brackets when running the command.
>>
>> Glad I could be helpful,
>>
>> -Paul
>> --
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Justina Lee <
>> justinale...@gmail.com>
>> *Sent:* Thursday, September 15, 2022 7:51 AM
>> *To:* Freesurfer support list 
>> *Subject:* Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command
>> not found
>>
>>
>> External Email - Use Caution
>>
>> Hi Paul,
>>
>> Thank you for your help tremendously throughout this process.
>>
>> Firstly, attached you will find the requested recon-all.log for the
>> subject 26 (originally located in the path
>> /home/ylee6/ADIPA_data/26/scripts), in which at the end of the log you
>> can see that the recon-all is completed successfully.
>>
>> Secondly, with the output from the 'env' command you can see it described
>> as such below:
>>
>> SHELL=/bin/bash
>> WSL_DISTRO_NAME=Ubuntu
>> OS=Linux
>> MINC_BIN_DIR=/usr/local/freesurfer/7.3.2/mni/bin
>> FSFAST_HOME=/usr/local/freesurfer/7.3.2/fsfast
>> FREESURFER=/usr/local/freesurfer/7.3.2
>> MNI_DATAPATH=/usr/local/freesurfer/7.3.2/mni/data
>> FS_OVERRIDE=0
>> NAME=LAPTOP-63HA9ANS
>> PWD=/home/ylee6/ADIPA_data/26/mri
>> LOGNAME=ylee6
>> FUNCTIONALS_DIR=/usr/local/freesurfer/7.3.2/sessions
>> MOTD_SHOWN=update-motd
>> HOME=/home/ylee6
>> LANG=C.UTF-8
>> WSL_INTEROP=/run/WSL/8_interop
>> MINC_LIB_DIR=/usr/local/freesurfer/7.3.2/mni/lib
>>
>> LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:

Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

[Justina Lee]

External Email - Use Caution

Hi Paul,

Thank you for all your help with some technical issues.
I was wondering if you could help me with one tiny issue I have been unable
to solve, which is the usage of freeview on my computer.
The installation has been completed successfully, but when I try to open
any data, I seem to not see anything. Upon trying again recently, now
opening freeview does not seem to work at all. (For example, trying to run
the command freeview -v T1.mgz does not produce a freeview to open up on
another window.)
Could you help me with this? I'm sorry for the troubles once more.

Sincerely,
Justina

On Thu, Sep 15, 2022 at 4:00 PM Wighton, Paul 
wrote:

> One more note:
>
> The command:
> export SUBJECTS_DIR=/home/ylee6/ADIPA_data
>
> May or may not work, depending on the type of shell environment you are
> using.  If it doesn't work, you can try:
> setenv SUBJECTS_DIR /home/ylee6/ADIPA_data
>
> To set the environment variable
>
> -Paul
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Wighton, Paul <
> pwigh...@mgh.harvard.edu>
> *Sent:* Thursday, September 15, 2022 9:56 AM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not
> found
>
> Hi Justina,
>
> Ok so on your computer, the subjects are located in
> /home/ylee6/ADIPA_data, but the SUBJECTS_DIR environment variable is set to
> /usr/local/freesurfer/7.3.2/subjects.
>
> There are two ways we can fix this.
>
> 1) We can change the SUBJECTS_DIR environment variable and then run
> segmentHA_T1.sh:
>
> export SUBJECTS_DIR=/home/ylee6/ADIPA_data
> segmentHA_T1.sh 26
>
> 2) Or, we can pass the subjects dir as a parameter to segmentHA_T1.sh,
> telling it to use that directory instead of the environment variable:
>
> segmentHA_T1.sh 26 /home/ylee6/ADIPA_data
>
> You were close with your command "segmentHA_T1.sh 26
> [/usr/local/freesurfer/7.3.2/subjects]"! Just FYI when you see a parameter
> in square brackets ([]) it means the parameter is optional, you shouldn't
> include the brackets when running the command.
>
> Glad I could be helpful,
>
> -Paul
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Justina Lee <
> justinale...@gmail.com>
> *Sent:* Thursday, September 15, 2022 7:51 AM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not
> found
>
>
> External Email - Use Caution
>
> Hi Paul,
>
> Thank you for your help tremendously throughout this process.
>
> Firstly, attached you will find the requested recon-all.log for the
> subject 26 (originally located in the path
> /home/ylee6/ADIPA_data/26/scripts), in which at the end of the log you
> can see that the recon-all is completed successfully.
>
> Secondly, with the output from the 'env' command you can see it described
> as such below:
>
> SHELL=/bin/bash
> WSL_DISTRO_NAME=Ubuntu
> OS=Linux
> MINC_BIN_DIR=/usr/local/freesurfer/7.3.2/mni/bin
> FSFAST_HOME=/usr/local/freesurfer/7.3.2/fsfast
> FREESURFER=/usr/local/freesurfer/7.3.2
> MNI_DATAPATH=/usr/local/freesurfer/7.3.2/mni/data
> FS_OVERRIDE=0
> NAME=LAPTOP-63HA9ANS
> PWD=/home/ylee6/ADIPA_data/26/mri
> LOGNAME=ylee6
> FUNCTIONALS_DIR=/usr/local/freesurfer/7.3.2/sessions
> MOTD_SHOWN=update-motd
> HOME=/home/ylee6
> LANG=C.UTF-8
> WSL_INTEROP=/run/WSL/8_interop
> MINC_LIB_DIR=/usr/local/freesurfer/7.3.2/mni/lib
>
> LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;

Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

[Wighton, Paul]

One more note:

The command:
export SUBJECTS_DIR=/home/ylee6/ADIPA_data

May or may not work, depending on the type of shell environment you are using.  
If it doesn't work, you can try:
setenv SUBJECTS_DIR /home/ylee6/ADIPA_data

To set the environment variable

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Wighton, Paul 

Sent: Thursday, September 15, 2022 9:56 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

Hi Justina,

Ok so on your computer, the subjects are located in /home/ylee6/ADIPA_data, but 
the SUBJECTS_DIR environment variable is set to 
/usr/local/freesurfer/7.3.2/subjects.

There are two ways we can fix this.

1) We can change the SUBJECTS_DIR environment variable and then run 
segmentHA_T1.sh:

export SUBJECTS_DIR=/home/ylee6/ADIPA_data
segmentHA_T1.sh 26

2) Or, we can pass the subjects dir as a parameter to segmentHA_T1.sh, telling 
it to use that directory instead of the environment variable:

segmentHA_T1.sh 26 /home/ylee6/ADIPA_data

You were close with your command "segmentHA_T1.sh 26 
[/usr/local/freesurfer/7.3.2/subjects]"! Just FYI when you see a parameter in 
square brackets ([]) it means the parameter is optional, you shouldn't include 
the brackets when running the command.

Glad I could be helpful,

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Justina Lee 

Sent: Thursday, September 15, 2022 7:51 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Hi Paul,

Thank you for your help tremendously throughout this process.

Firstly, attached you will find the requested recon-all.log for the subject 
26 (originally located in the path /home/ylee6/ADIPA_data/26/scripts), 
in which at the end of the log you can see that the recon-all is completed 
successfully.

Secondly, with the output from the 'env' command you can see it described as 
such below:

SHELL=/bin/bash
WSL_DISTRO_NAME=Ubuntu
OS=Linux
MINC_BIN_DIR=/usr/local/freesurfer/7.3.2/mni/bin
FSFAST_HOME=/usr/local/freesurfer/7.3.2/fsfast
FREESURFER=/usr/local/freesurfer/7.3.2
MNI_DATAPATH=/usr/local/freesurfer/7.3.2/mni/data
FS_OVERRIDE=0
NAME=LAPTOP-63HA9ANS
PWD=/home/ylee6/ADIPA_data/26/mri
LOGNAME=ylee6
FUNCTIONALS_DIR=/usr/local/freesurfer/7.3.2/sessions
MOTD_SHOWN=update-motd
HOME=/home/ylee6
LANG=C.UTF-8
WSL_INTEROP=/run/WSL/8_interop
MINC_LIB_DIR=/usr/local/freesurfer/7.3.2/mni/lib
LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36:
WAYLAND_DISPLAY=wayland-0
FMRI_ANALYSIS_DIR=/usr/local/freesurfer/7.3.2/fsfast
MNI_DIR=/usr/local/freesurfer/7.3.2/mni
PERL5LIB=/usr/local/freesurfer/7.3.2/mni/share/perl5
MNI_PERL5LIB=/usr/local/freesurfer/7.3.2/mni/share/perl5
FREESURFER_HOME=/usr/local/freesurfer/7.3.2
LESSCLOSE=/usr/bin/lesspipe %s %s
LOCAL_DIR=/usr/local/freesurfer/7.3.2/local
TERM=xterm-256color
FIX_VERTEX_AREA=
LESSOPEN=| /usr/bin/lesspipe %s
USER=ylee6
DISPLAY=172.25.144.1:0<http://secure-web.cisco.com/1-hejosJTLRC2vV-OfdCSe_uY8hHvMUDjci5bJsNGZn55Ex_VuIMtvmOuJdpL7qWdzXWDGWXTu8KGwGjHhDnfNs_Oz9looUNIOEBEBDEhKbiE_unv86fZj2sikQ0C0-tHyqn_l6wkDU_YWnG6DV3QHzjtYNloKKHEuKAgZ0pB0BV4tlM4606CV71h7g44f_CnbhyUAiGY6ITBFhskq654vl-8YehA-4iHy8efSL8oarabfltq8DZl-xQhNFFPsqGFEXKF7G2k0L2szdfOQvb6GN2jH9O1S832tDcli4qEUuOwNLR1x02kQiybtiDrvGm-/http%3A%2F%2F172.25.144.1%3A0>
SHLVL=1
SUBJECTS_DIR=/usr/local/freesurfe

Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

[Wighton, Paul]

Hi Justina,

Ok so on your computer, the subjects are located in /home/ylee6/ADIPA_data, but 
the SUBJECTS_DIR environment variable is set to 
/usr/local/freesurfer/7.3.2/subjects.

There are two ways we can fix this.

1) We can change the SUBJECTS_DIR environment variable and then run 
segmentHA_T1.sh:

export SUBJECTS_DIR=/home/ylee6/ADIPA_data
segmentHA_T1.sh 26

2) Or, we can pass the subjects dir as a parameter to segmentHA_T1.sh, telling 
it to use that directory instead of the environment variable:

segmentHA_T1.sh 26 /home/ylee6/ADIPA_data

You were close with your command "segmentHA_T1.sh 26 
[/usr/local/freesurfer/7.3.2/subjects]"! Just FYI when you see a parameter in 
square brackets ([]) it means the parameter is optional, you shouldn't include 
the brackets when running the command.

Glad I could be helpful,

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Justina Lee 

Sent: Thursday, September 15, 2022 7:51 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Hi Paul,

Thank you for your help tremendously throughout this process.

Firstly, attached you will find the requested recon-all.log for the subject 
26 (originally located in the path /home/ylee6/ADIPA_data/26/scripts), 
in which at the end of the log you can see that the recon-all is completed 
successfully.

Secondly, with the output from the 'env' command you can see it described as 
such below:

SHELL=/bin/bash
WSL_DISTRO_NAME=Ubuntu
OS=Linux
MINC_BIN_DIR=/usr/local/freesurfer/7.3.2/mni/bin
FSFAST_HOME=/usr/local/freesurfer/7.3.2/fsfast
FREESURFER=/usr/local/freesurfer/7.3.2
MNI_DATAPATH=/usr/local/freesurfer/7.3.2/mni/data
FS_OVERRIDE=0
NAME=LAPTOP-63HA9ANS
PWD=/home/ylee6/ADIPA_data/26/mri
LOGNAME=ylee6
FUNCTIONALS_DIR=/usr/local/freesurfer/7.3.2/sessions
MOTD_SHOWN=update-motd
HOME=/home/ylee6
LANG=C.UTF-8
WSL_INTEROP=/run/WSL/8_interop
MINC_LIB_DIR=/usr/local/freesurfer/7.3.2/mni/lib
LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36:
WAYLAND_DISPLAY=wayland-0
FMRI_ANALYSIS_DIR=/usr/local/freesurfer/7.3.2/fsfast
MNI_DIR=/usr/local/freesurfer/7.3.2/mni
PERL5LIB=/usr/local/freesurfer/7.3.2/mni/share/perl5
MNI_PERL5LIB=/usr/local/freesurfer/7.3.2/mni/share/perl5
FREESURFER_HOME=/usr/local/freesurfer/7.3.2
LESSCLOSE=/usr/bin/lesspipe %s %s
LOCAL_DIR=/usr/local/freesurfer/7.3.2/local
TERM=xterm-256color
FIX_VERTEX_AREA=
LESSOPEN=| /usr/bin/lesspipe %s
USER=ylee6
DISPLAY=172.25.144.1:0<http://secure-web.cisco.com/1-hejosJTLRC2vV-OfdCSe_uY8hHvMUDjci5bJsNGZn55Ex_VuIMtvmOuJdpL7qWdzXWDGWXTu8KGwGjHhDnfNs_Oz9looUNIOEBEBDEhKbiE_unv86fZj2sikQ0C0-tHyqn_l6wkDU_YWnG6DV3QHzjtYNloKKHEuKAgZ0pB0BV4tlM4606CV71h7g44f_CnbhyUAiGY6ITBFhskq654vl-8YehA-4iHy8efSL8oarabfltq8DZl-xQhNFFPsqGFEXKF7G2k0L2szdfOQvb6GN2jH9O1S832tDcli4qEUuOwNLR1x02kQiybtiDrvGm-/http%3A%2F%2F172.25.144.1%3A0>
SHLVL=1
SUBJECTS_DIR=/usr/local/freesurfer/7.3.2/subjects
XDG_RUNTIME_DIR=/home/ylee6/.xdg
FS_LICENSE=/home/ylee6/license.txt
WSLENV=
XDG_DATA_DIRS=/usr/local/share:/usr/share:/var/lib/snapd/desktop
PATH=/usr/local/freesurfer/7.3.2/bin:/usr/local/freesurfer/7.3.2/fsfast/bin:/usr/local/freesurfer/7.3.2/tktools:/usr/local/freesurfer/7.3.2/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/lib/wsl/lib:/mnt/c/WINDOWS/system32:/mnt/c/WINDOWS:/mnt/c/WINDOWS/System32/Wbem:/mnt/c/WINDOWS/System32/WindowsPowerShell/v1.0

Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

[Wighton, Paul]

Hi Justina,

Can you send the following:
  - The recon-all.log file for the subject you are trying to run through 
segmentHA_T1.sh
  - The output from running the `env` command
  - The command you are using to invoke segmentHA_T1.sh

My guess is that the SUBJECTS_DIR environment variable isn't set correctly, but 
we should also double check that recon-all completed successfully.

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Justina Lee 

Sent: Wednesday, September 14, 2022 3:56 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Hi Paul,

This seems to have done the trick. Thank you for guiding me through this 
process, I really appreciate all your help.

My last question refers to this comment when trying to run the segmentHA_T1.sh 
command:

Cannot find wmparc.mgz or norm.mgz or talairach.xfm for the subject.
Has the subject been procesed with recon-all?

I am sure that I am referring to the right path where the files are located as 
well as processing the subject with recon-all already. Is there something that 
I am missing?

Thank you so much for your time.

Sincerely,
Justina


On Tue, Sep 13, 2022 at 9:05 PM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
I think we are on the right track, but it looks like there was a space between 
FREESURFER_HOME and the equal (=) sign? It also looks like there was no space 
between '$FREESURFER_HOME' and './fs_install_mcr'?

The command should be copied exactly as written:
sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b

-Paul


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Justina Lee 
mailto:justinale...@gmail.com>>
Sent: Tuesday, September 13, 2022 2:57 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Hi Paul,

I have taken your advice and run the command as shown below:

ylee6@LAPTOP-63HA9ANS:~$ cd /usr/local/freesurfer/7.3.2/bin
ylee6@LAPTOP-63HA9ANS:/usr/local/freesurfer/7.3.2/bin$ sudo FREESURFER_HOME 
=$FREESURFER_HOME./fs_install_mcr R2019b
sudo: FREESURFER_HOME: command not found

The same problem persists yet again :( Does the problem lie somewhere else?

Sincerely,
Justina

On Tue, Sep 13, 2022 at 8:49 PM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
Ah ok, let's try this:

cd /usr/local/freesurfer/7.3.2/bin
sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b

We are appending `./` to fs_install_mcr to tell it it's in the same directory.  
We are also passing the definition of FREESURFER_HOME into the 'sudo'ed' 
environment, because the install script relies on that.

-Paul

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Justina Lee 
mailto:justinale...@gmail.com>>
Sent: Tuesday, September 13, 2022 2:37 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Hi Paul,

I have entered the command under this directory 
ylee6@LAPTOP-63HA9ANS:/usr/local/freesurfer/7.3.2/bin$ sudo fs_install_mcr 
R2019b and the following error persists. (sudo: fs_install_mcr: command not 
found)

Could there be a reason for this?

Sincerely,
Justina

On Tue, Sep 13, 2022 at 8:33 PM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
Hi Justina,

Are you in the right directory (/usr/local/freesurfer/7.3.2/bin)?

Can you try `cd /usr/local/freesurfer/7.3.2/bin` then `sudo fs_install_mcr 
R2019b`?

-Paul


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Justina Lee 
mailto:justinale...@gmail.com>>
Sent: Tuesday, September 13, 2022 2:28 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Hi Paul,

When I try to run the installation command with sudo, the following error 
command shows:

sudo: fs_install_mcr: command not found

I'm terribly sorry for the inconvenience.

Sincerely,
Justina

On Tue, Sep 13, 2022 at 8:23 PM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
Hi Justina,

Ok so it looks like the install script is getting further and has extracted the 
matlab runtime environment into a temporary directory 
(/tmp/tmp.nGZQXYOgR8/install-target/v97

Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

[Justina Lee]

External Email - Use Caution

Hi Paul,

This seems to have done the trick. Thank you for guiding me through this
process, I really appreciate all your help.

My last question refers to this comment when trying to run the
segmentHA_T1.sh command:

Cannot find wmparc.mgz or norm.mgz or talairach.xfm for the subject.
Has the subject been procesed with recon-all?

I am sure that I am referring to the right path where the files are located
as well as processing the subject with recon-all already. Is there
something that I am missing?

Thank you so much for your time.

Sincerely,
Justina


On Tue, Sep 13, 2022 at 9:05 PM Wighton, Paul 
wrote:

> I think we are on the right track, but it looks like there was a space
> between FREESURFER_HOME and the equal (=) sign? It also looks like there
> was no space between '$FREESURFER_HOME' and './fs_install_mcr'?
>
> The command should be copied exactly as written:
> sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b
>
> -Paul
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Justina Lee <
> justinale...@gmail.com>
> *Sent:* Tuesday, September 13, 2022 2:57 PM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not
> found
>
>
> External Email - Use Caution
>
> Hi Paul,
>
> I have taken your advice and run the command as shown below:
>
> ylee6@LAPTOP-63HA9ANS:~$ cd /usr/local/freesurfer/7.3.2/bin
> ylee6@LAPTOP-63HA9ANS:/usr/local/freesurfer/7.3.2/bin$ sudo
> FREESURFER_HOME =$FREESURFER_HOME./fs_install_mcr R2019b
> sudo: FREESURFER_HOME: command not found
>
> The same problem persists yet again :( Does the problem lie somewhere else?
>
> Sincerely,
> Justina
>
> On Tue, Sep 13, 2022 at 8:49 PM Wighton, Paul 
> wrote:
>
> Ah ok, let's try this:
>
> cd /usr/local/freesurfer/7.3.2/bin
> sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b
>
> We are appending `./` to fs_install_mcr to tell it it's in the same
> directory.  We are also passing the definition of FREESURFER_HOME into the
> 'sudo'ed' environment, because the install script relies on that.
>
> -Paul
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Justina Lee <
> justinale...@gmail.com>
> *Sent:* Tuesday, September 13, 2022 2:37 PM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not
> found
>
>
> External Email - Use Caution
>
> Hi Paul,
>
> I have entered the command under this directory 
> ylee6@LAPTOP-63HA9ANS:/usr/local/freesurfer/7.3.2/bin$
> sudo fs_install_mcr R2019b and the following error persists. (sudo:
> fs_install_mcr: command not found)
>
> Could there be a reason for this?
>
> Sincerely,
> Justina
>
> On Tue, Sep 13, 2022 at 8:33 PM Wighton, Paul 
> wrote:
>
> Hi Justina,
>
> Are you in the right directory (/usr/local/freesurfer/7.3.2/bin)?
>
> Can you try `cd /usr/local/freesurfer/7.3.2/bin` then `sudo fs_install_mcr
> R2019b`?
>
> -Paul
>
> ----------
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Justina Lee <
> justinale...@gmail.com>
> *Sent:* Tuesday, September 13, 2022 2:28 PM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not
> found
>
>
> External Email - Use Caution
>
> Hi Paul,
>
> When I try to run the installation command with sudo, the following error
> command shows:
>
> sudo: fs_install_mcr: command not found
>
> I'm terribly sorry for the inconvenience.
>
> Sincerely,
> Justina
>
> On Tue, Sep 13, 2022 at 8:23 PM Wighton, Paul 
> wrote:
>
> Hi Justina,
>
> Ok so it looks like the install script is getting further and has
> extracted the matlab runtime environment into a temporary directory
> (/tmp/tmp.nGZQXYOgR8/install-target/v97) but during the final step, it is
> trying to move that temporary directory to a location inside the FreeSurfer
> directory (/usr/local/freesurfer/7.3.2/MCRv97) and it is once again running
> into a 'Permission Denied' error.
>
> Can you try re-installing the matlab runtime by running `sudo
> fs_install_mcr R2019b` so that the install script has permissions to write
> to the FreeSurfer directory?
>
> -Paul
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Just

Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

[Wighton, Paul]

I think we are on the right track, but it looks like there was a space between 
FREESURFER_HOME and the equal (=) sign? It also looks like there was no space 
between '$FREESURFER_HOME' and './fs_install_mcr'?

The command should be copied exactly as written:
sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Justina Lee 

Sent: Tuesday, September 13, 2022 2:57 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Hi Paul,

I have taken your advice and run the command as shown below:

ylee6@LAPTOP-63HA9ANS:~$ cd /usr/local/freesurfer/7.3.2/bin
ylee6@LAPTOP-63HA9ANS:/usr/local/freesurfer/7.3.2/bin$ sudo FREESURFER_HOME 
=$FREESURFER_HOME./fs_install_mcr R2019b
sudo: FREESURFER_HOME: command not found

The same problem persists yet again :( Does the problem lie somewhere else?

Sincerely,
Justina

On Tue, Sep 13, 2022 at 8:49 PM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
Ah ok, let's try this:

cd /usr/local/freesurfer/7.3.2/bin
sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b

We are appending `./` to fs_install_mcr to tell it it's in the same directory.  
We are also passing the definition of FREESURFER_HOME into the 'sudo'ed' 
environment, because the install script relies on that.

-Paul

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Justina Lee 
mailto:justinale...@gmail.com>>
Sent: Tuesday, September 13, 2022 2:37 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Hi Paul,

I have entered the command under this directory 
ylee6@LAPTOP-63HA9ANS:/usr/local/freesurfer/7.3.2/bin$ sudo fs_install_mcr 
R2019b and the following error persists. (sudo: fs_install_mcr: command not 
found)

Could there be a reason for this?

Sincerely,
Justina

On Tue, Sep 13, 2022 at 8:33 PM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
Hi Justina,

Are you in the right directory (/usr/local/freesurfer/7.3.2/bin)?

Can you try `cd /usr/local/freesurfer/7.3.2/bin` then `sudo fs_install_mcr 
R2019b`?

-Paul


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Justina Lee 
mailto:justinale...@gmail.com>>
Sent: Tuesday, September 13, 2022 2:28 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Hi Paul,

When I try to run the installation command with sudo, the following error 
command shows:

sudo: fs_install_mcr: command not found

I'm terribly sorry for the inconvenience.

Sincerely,
Justina

On Tue, Sep 13, 2022 at 8:23 PM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
Hi Justina,

Ok so it looks like the install script is getting further and has extracted the 
matlab runtime environment into a temporary directory 
(/tmp/tmp.nGZQXYOgR8/install-target/v97) but during the final step, it is 
trying to move that temporary directory to a location inside the FreeSurfer 
directory (/usr/local/freesurfer/7.3.2/MCRv97) and it is once again running 
into a 'Permission Denied' error.

Can you try re-installing the matlab runtime by running `sudo fs_install_mcr 
R2019b` so that the install script has permissions to write to the FreeSurfer 
directory?

-Paul


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Justina Lee 
mailto:justinale...@gmail.com>>
Sent: Tuesday, September 13, 2022 1:58 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Thank you Paul for your help!

This seems to have solved the issue, as I can now run the command 
fs_install_mcr R2019b. It has ended successfully with this end message stated 
below:



mv: cannot move '/tmp/tmp.nGZQXYOgR8/install-target/v97' to 
'/usr/local/freesurfer/7.3.2/MCRv97': Permission denied



I think this problem persists with my next issue, which is using the command 
segmentHA_T1.sh. When I try to run this command again it gives me the following 
error:



ERROR: cannot find Matlab 2019b runtime in location:



/usr/local/freesurfer/7.3.2/MCRv97



It is looking for either:

  bin/glnxa64/libmwlaunchermain.so(Linux 64b) or

Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

[Justina Lee]

External Email - Use Caution

Hi Paul,

I have taken your advice and run the command as shown below:

ylee6@LAPTOP-63HA9ANS:~$ cd /usr/local/freesurfer/7.3.2/bin
ylee6@LAPTOP-63HA9ANS:/usr/local/freesurfer/7.3.2/bin$ sudo FREESURFER_HOME
=$FREESURFER_HOME./fs_install_mcr R2019b
sudo: FREESURFER_HOME: command not found

The same problem persists yet again :( Does the problem lie somewhere else?

Sincerely,
Justina

On Tue, Sep 13, 2022 at 8:49 PM Wighton, Paul 
wrote:

> Ah ok, let's try this:
>
> cd /usr/local/freesurfer/7.3.2/bin
> sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b
>
> We are appending `./` to fs_install_mcr to tell it it's in the same
> directory.  We are also passing the definition of FREESURFER_HOME into the
> 'sudo'ed' environment, because the install script relies on that.
>
> -Paul
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Justina Lee <
> justinale...@gmail.com>
> *Sent:* Tuesday, September 13, 2022 2:37 PM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not
> found
>
>
> External Email - Use Caution
>
> Hi Paul,
>
> I have entered the command under this directory 
> ylee6@LAPTOP-63HA9ANS:/usr/local/freesurfer/7.3.2/bin$
> sudo fs_install_mcr R2019b and the following error persists. (sudo:
> fs_install_mcr: command not found)
>
> Could there be a reason for this?
>
> Sincerely,
> Justina
>
> On Tue, Sep 13, 2022 at 8:33 PM Wighton, Paul 
> wrote:
>
> Hi Justina,
>
> Are you in the right directory (/usr/local/freesurfer/7.3.2/bin)?
>
> Can you try `cd /usr/local/freesurfer/7.3.2/bin` then `sudo fs_install_mcr
> R2019b`?
>
> -Paul
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Justina Lee <
> justinale...@gmail.com>
> *Sent:* Tuesday, September 13, 2022 2:28 PM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not
> found
>
>
> External Email - Use Caution
>
> Hi Paul,
>
> When I try to run the installation command with sudo, the following error
> command shows:
>
> sudo: fs_install_mcr: command not found
>
> I'm terribly sorry for the inconvenience.
>
> Sincerely,
> Justina
>
> On Tue, Sep 13, 2022 at 8:23 PM Wighton, Paul 
> wrote:
>
> Hi Justina,
>
> Ok so it looks like the install script is getting further and has
> extracted the matlab runtime environment into a temporary directory
> (/tmp/tmp.nGZQXYOgR8/install-target/v97) but during the final step, it is
> trying to move that temporary directory to a location inside the FreeSurfer
> directory (/usr/local/freesurfer/7.3.2/MCRv97) and it is once again running
> into a 'Permission Denied' error.
>
> Can you try re-installing the matlab runtime by running `sudo
> fs_install_mcr R2019b` so that the install script has permissions to write
> to the FreeSurfer directory?
>
> -Paul
>
> ----------
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Justina Lee <
> justinale...@gmail.com>
> *Sent:* Tuesday, September 13, 2022 1:58 PM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not
> found
>
>
> External Email - Use Caution
>
> Thank you Paul for your help!
>
>
> This seems to have solved the issue, as I can now run the command
> fs_install_mcr R2019b. It has ended successfully with this end message
> stated below:
>
>
>
> mv: cannot move '/tmp/tmp.nGZQXYOgR8/install-target/v97' to
> '/usr/local/freesurfer/7.3.2/MCRv97': Permission denied
>
>
>
> I think this problem persists with my next issue, which is using the
> command segmentHA_T1.sh. When I try to run this command again it gives me
> the following error:
>
>
>
> ERROR: cannot find Matlab 2019b runtime in location:
>
>
>
> /usr/local/freesurfer/7.3.2/MCRv97
>
>
>
> It is looking for either:
>
>   bin/glnxa64/libmwlaunchermain.so(Linux 64b) or
>
>   bin/maci64/libmwlaunchermain.dylib (Mac 64b)
>
>
>
> The hippocampal/amygdala and brainstem modules require the (free) Matlab
> runtime.
>
> You will need to download the Matlab Compiler Runtime (MCR) for Matlab
> 2019b.
>
> To do so, please run the following command (you might need root
> permissions):
>
>
>
> fs_install_mcr R2019b
>
>
>
> I have seen that the path

Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

[Wighton, Paul]

Ah ok, let's try this:

cd /usr/local/freesurfer/7.3.2/bin
sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b

We are appending `./` to fs_install_mcr to tell it it's in the same directory.  
We are also passing the definition of FREESURFER_HOME into the 'sudo'ed' 
environment, because the install script relies on that.

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Justina Lee 

Sent: Tuesday, September 13, 2022 2:37 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Hi Paul,

I have entered the command under this directory 
ylee6@LAPTOP-63HA9ANS:/usr/local/freesurfer/7.3.2/bin$ sudo fs_install_mcr 
R2019b and the following error persists. (sudo: fs_install_mcr: command not 
found)

Could there be a reason for this?

Sincerely,
Justina

On Tue, Sep 13, 2022 at 8:33 PM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
Hi Justina,

Are you in the right directory (/usr/local/freesurfer/7.3.2/bin)?

Can you try `cd /usr/local/freesurfer/7.3.2/bin` then `sudo fs_install_mcr 
R2019b`?

-Paul


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Justina Lee 
mailto:justinale...@gmail.com>>
Sent: Tuesday, September 13, 2022 2:28 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Hi Paul,

When I try to run the installation command with sudo, the following error 
command shows:

sudo: fs_install_mcr: command not found

I'm terribly sorry for the inconvenience.

Sincerely,
Justina

On Tue, Sep 13, 2022 at 8:23 PM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
Hi Justina,

Ok so it looks like the install script is getting further and has extracted the 
matlab runtime environment into a temporary directory 
(/tmp/tmp.nGZQXYOgR8/install-target/v97) but during the final step, it is 
trying to move that temporary directory to a location inside the FreeSurfer 
directory (/usr/local/freesurfer/7.3.2/MCRv97) and it is once again running 
into a 'Permission Denied' error.

Can you try re-installing the matlab runtime by running `sudo fs_install_mcr 
R2019b` so that the install script has permissions to write to the FreeSurfer 
directory?

-Paul


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Justina Lee 
mailto:justinale...@gmail.com>>
Sent: Tuesday, September 13, 2022 1:58 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Thank you Paul for your help!

This seems to have solved the issue, as I can now run the command 
fs_install_mcr R2019b. It has ended successfully with this end message stated 
below:



mv: cannot move '/tmp/tmp.nGZQXYOgR8/install-target/v97' to 
'/usr/local/freesurfer/7.3.2/MCRv97': Permission denied



I think this problem persists with my next issue, which is using the command 
segmentHA_T1.sh. When I try to run this command again it gives me the following 
error:



ERROR: cannot find Matlab 2019b runtime in location:



/usr/local/freesurfer/7.3.2/MCRv97



It is looking for either:

  bin/glnxa64/libmwlaunchermain.so(Linux 64b) or

  bin/maci64/libmwlaunchermain.dylib (Mac 64b)



The hippocampal/amygdala and brainstem modules require the (free) Matlab 
runtime.

You will need to download the Matlab Compiler Runtime (MCR) for Matlab 2019b.

To do so, please run the following command (you might need root permissions):



fs_install_mcr R2019b



I have seen that the pathway for fs_install_mcr is located in the 
usr/local/freesurfer/7.3.2 instead of in the location stated in the error 
above. When I try to search this location there is no such existing directory. 
This can be the same for bin/glnxa64/libmwlaunchermain.so.



Do I need to create a new file for where the runtime should be stored? Or 
create a file for the bin/glnxa64/libmwlaunchermain.so to be stored? Should the 
fs_installl_mcr R2019b be stored under bin for this command to work?

Hope you can continue to help me with my follow-up issue, I appreciate it a lot.

Thank you so much.



Sincerely,
Justina

On Tue, Sep 13, 2022 at 4:35 PM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
Hi Justina,

It looks like the matlab installer is trying to use unzip but it can't find it.

Can you try running:
`sudo apt-get install unzip`

To install unzip then try the matlab installer again?

-Paul

Fr

Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

[Justina Lee]

External Email - Use Caution

Hi Paul,

I have entered the command under this directory
ylee6@LAPTOP-63HA9ANS:/usr/local/freesurfer/7.3.2/bin$
sudo fs_install_mcr R2019b and the following error persists. (sudo:
fs_install_mcr: command not found)

Could there be a reason for this?

Sincerely,
Justina

On Tue, Sep 13, 2022 at 8:33 PM Wighton, Paul 
wrote:

> Hi Justina,
>
> Are you in the right directory (/usr/local/freesurfer/7.3.2/bin)?
>
> Can you try `cd /usr/local/freesurfer/7.3.2/bin` then `sudo fs_install_mcr
> R2019b`?
>
> -Paul
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Justina Lee <
> justinale...@gmail.com>
> *Sent:* Tuesday, September 13, 2022 2:28 PM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not
> found
>
>
> External Email - Use Caution
>
> Hi Paul,
>
> When I try to run the installation command with sudo, the following error
> command shows:
>
> sudo: fs_install_mcr: command not found
>
> I'm terribly sorry for the inconvenience.
>
> Sincerely,
> Justina
>
> On Tue, Sep 13, 2022 at 8:23 PM Wighton, Paul 
> wrote:
>
> Hi Justina,
>
> Ok so it looks like the install script is getting further and has
> extracted the matlab runtime environment into a temporary directory
> (/tmp/tmp.nGZQXYOgR8/install-target/v97) but during the final step, it is
> trying to move that temporary directory to a location inside the FreeSurfer
> directory (/usr/local/freesurfer/7.3.2/MCRv97) and it is once again running
> into a 'Permission Denied' error.
>
> Can you try re-installing the matlab runtime by running `sudo
> fs_install_mcr R2019b` so that the install script has permissions to write
> to the FreeSurfer directory?
>
> -Paul
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Justina Lee <
> justinale...@gmail.com>
> *Sent:* Tuesday, September 13, 2022 1:58 PM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not
> found
>
>
> External Email - Use Caution
>
> Thank you Paul for your help!
>
>
> This seems to have solved the issue, as I can now run the command
> fs_install_mcr R2019b. It has ended successfully with this end message
> stated below:
>
>
>
> mv: cannot move '/tmp/tmp.nGZQXYOgR8/install-target/v97' to
> '/usr/local/freesurfer/7.3.2/MCRv97': Permission denied
>
>
>
> I think this problem persists with my next issue, which is using the
> command segmentHA_T1.sh. When I try to run this command again it gives me
> the following error:
>
>
>
> ERROR: cannot find Matlab 2019b runtime in location:
>
>
>
> /usr/local/freesurfer/7.3.2/MCRv97
>
>
>
> It is looking for either:
>
>   bin/glnxa64/libmwlaunchermain.so(Linux 64b) or
>
>   bin/maci64/libmwlaunchermain.dylib (Mac 64b)
>
>
>
> The hippocampal/amygdala and brainstem modules require the (free) Matlab
> runtime.
>
> You will need to download the Matlab Compiler Runtime (MCR) for Matlab
> 2019b.
>
> To do so, please run the following command (you might need root
> permissions):
>
>
>
> fs_install_mcr R2019b
>
>
>
> I have seen that the pathway for fs_install_mcr is located in the
> usr/local/freesurfer/7.3.2 instead of in the location stated in the error
> above. When I try to search this location there is no such existing
> directory. This can be the same for bin/glnxa64/libmwlaunchermain.so.
>
>
>
> Do I need to create a new file for where the runtime should be stored? Or
> create a file for the bin/glnxa64/libmwlaunchermain.so to be stored? Should
> the fs_installl_mcr R2019b be stored under bin for this command to work?
>
> Hope you can continue to help me with my follow-up issue, I appreciate it
> a lot.
>
> Thank you so much.
>
>
>
> Sincerely,
> Justina
>
> On Tue, Sep 13, 2022 at 4:35 PM Wighton, Paul 
> wrote:
>
> Hi Justina,
>
> It looks like the matlab installer is trying to use unzip but it can't
> find it.
>
> Can you try running:
> `sudo apt-get install unzip`
>
> To install unzip then try the matlab installer again?
>
> -Paul
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of You Na Lee <
> justinale...@gmail.com>
> *Sent:* Tuesday, September 13, 2022 9:01 AM
> *To:* freesurfer@nmr.mgh.harvard.edu 
> *Sub

Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

[Wighton, Paul]

Hi Justina,

Are you in the right directory (/usr/local/freesurfer/7.3.2/bin)?

Can you try `cd /usr/local/freesurfer/7.3.2/bin` then `sudo fs_install_mcr 
R2019b`?

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Justina Lee 

Sent: Tuesday, September 13, 2022 2:28 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Hi Paul,

When I try to run the installation command with sudo, the following error 
command shows:

sudo: fs_install_mcr: command not found

I'm terribly sorry for the inconvenience.

Sincerely,
Justina

On Tue, Sep 13, 2022 at 8:23 PM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
Hi Justina,

Ok so it looks like the install script is getting further and has extracted the 
matlab runtime environment into a temporary directory 
(/tmp/tmp.nGZQXYOgR8/install-target/v97) but during the final step, it is 
trying to move that temporary directory to a location inside the FreeSurfer 
directory (/usr/local/freesurfer/7.3.2/MCRv97) and it is once again running 
into a 'Permission Denied' error.

Can you try re-installing the matlab runtime by running `sudo fs_install_mcr 
R2019b` so that the install script has permissions to write to the FreeSurfer 
directory?

-Paul


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Justina Lee 
mailto:justinale...@gmail.com>>
Sent: Tuesday, September 13, 2022 1:58 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Thank you Paul for your help!

This seems to have solved the issue, as I can now run the command 
fs_install_mcr R2019b. It has ended successfully with this end message stated 
below:



mv: cannot move '/tmp/tmp.nGZQXYOgR8/install-target/v97' to 
'/usr/local/freesurfer/7.3.2/MCRv97': Permission denied



I think this problem persists with my next issue, which is using the command 
segmentHA_T1.sh. When I try to run this command again it gives me the following 
error:



ERROR: cannot find Matlab 2019b runtime in location:



/usr/local/freesurfer/7.3.2/MCRv97



It is looking for either:

  bin/glnxa64/libmwlaunchermain.so(Linux 64b) or

  bin/maci64/libmwlaunchermain.dylib (Mac 64b)



The hippocampal/amygdala and brainstem modules require the (free) Matlab 
runtime.

You will need to download the Matlab Compiler Runtime (MCR) for Matlab 2019b.

To do so, please run the following command (you might need root permissions):



fs_install_mcr R2019b



I have seen that the pathway for fs_install_mcr is located in the 
usr/local/freesurfer/7.3.2 instead of in the location stated in the error 
above. When I try to search this location there is no such existing directory. 
This can be the same for bin/glnxa64/libmwlaunchermain.so.



Do I need to create a new file for where the runtime should be stored? Or 
create a file for the bin/glnxa64/libmwlaunchermain.so to be stored? Should the 
fs_installl_mcr R2019b be stored under bin for this command to work?

Hope you can continue to help me with my follow-up issue, I appreciate it a lot.

Thank you so much.



Sincerely,
Justina

On Tue, Sep 13, 2022 at 4:35 PM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
Hi Justina,

It looks like the matlab installer is trying to use unzip but it can't find it.

Can you try running:
`sudo apt-get install unzip`

To install unzip then try the matlab installer again?

-Paul

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of You Na Lee mailto:justinale...@gmail.com>>
Sent: Tuesday, September 13, 2022 9:01 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

To whom it may concern,



Apologies for my first post, I was a little bit confounded as to how I can 
reach for help.


I would like to use the segmentation of hippocampal subfields and the nuclei of 
the amygdala.
Currently, I am working with Ubuntu on windows with Freesurfer 7.3.2.

I am trying to install MATLAB Runtime 2019b to run the command segmentHA_T1.sh 
for the segmentation as described above. The following command shows the 
corresponding error:



ylee6@LAPTOP-63HA9ANS: /usr/local/freesurfer/7.3.2/bin$ fs_install_mcr R2019b

  % Total% Received % Xferd  Average Speed   TimeTime Time  Current

 Dload  Upload   Total   SpentLeft  Spee

Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

[Justina Lee]

External Email - Use Caution

Hi Paul,

When I try to run the installation command with sudo, the following error
command shows:

sudo: fs_install_mcr: command not found

I'm terribly sorry for the inconvenience.

Sincerely,
Justina

On Tue, Sep 13, 2022 at 8:23 PM Wighton, Paul 
wrote:

> Hi Justina,
>
> Ok so it looks like the install script is getting further and has
> extracted the matlab runtime environment into a temporary directory
> (/tmp/tmp.nGZQXYOgR8/install-target/v97) but during the final step, it is
> trying to move that temporary directory to a location inside the FreeSurfer
> directory (/usr/local/freesurfer/7.3.2/MCRv97) and it is once again running
> into a 'Permission Denied' error.
>
> Can you try re-installing the matlab runtime by running `sudo
> fs_install_mcr R2019b` so that the install script has permissions to write
> to the FreeSurfer directory?
>
> -Paul
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Justina Lee <
> justinale...@gmail.com>
> *Sent:* Tuesday, September 13, 2022 1:58 PM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not
> found
>
>
> External Email - Use Caution
>
> Thank you Paul for your help!
>
>
> This seems to have solved the issue, as I can now run the command
> fs_install_mcr R2019b. It has ended successfully with this end message
> stated below:
>
>
>
> mv: cannot move '/tmp/tmp.nGZQXYOgR8/install-target/v97' to
> '/usr/local/freesurfer/7.3.2/MCRv97': Permission denied
>
>
>
> I think this problem persists with my next issue, which is using the
> command segmentHA_T1.sh. When I try to run this command again it gives me
> the following error:
>
>
>
> ERROR: cannot find Matlab 2019b runtime in location:
>
>
>
> /usr/local/freesurfer/7.3.2/MCRv97
>
>
>
> It is looking for either:
>
>   bin/glnxa64/libmwlaunchermain.so(Linux 64b) or
>
>   bin/maci64/libmwlaunchermain.dylib (Mac 64b)
>
>
>
> The hippocampal/amygdala and brainstem modules require the (free) Matlab
> runtime.
>
> You will need to download the Matlab Compiler Runtime (MCR) for Matlab
> 2019b.
>
> To do so, please run the following command (you might need root
> permissions):
>
>
>
> fs_install_mcr R2019b
>
>
>
> I have seen that the pathway for fs_install_mcr is located in the
> usr/local/freesurfer/7.3.2 instead of in the location stated in the error
> above. When I try to search this location there is no such existing
> directory. This can be the same for bin/glnxa64/libmwlaunchermain.so.
>
>
>
> Do I need to create a new file for where the runtime should be stored? Or
> create a file for the bin/glnxa64/libmwlaunchermain.so to be stored? Should
> the fs_installl_mcr R2019b be stored under bin for this command to work?
>
> Hope you can continue to help me with my follow-up issue, I appreciate it
> a lot.
>
> Thank you so much.
>
>
>
> Sincerely,
> Justina
>
> On Tue, Sep 13, 2022 at 4:35 PM Wighton, Paul 
> wrote:
>
> Hi Justina,
>
> It looks like the matlab installer is trying to use unzip but it can't
> find it.
>
> Can you try running:
> `sudo apt-get install unzip`
>
> To install unzip then try the matlab installer again?
>
> -Paul
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of You Na Lee <
> justinale...@gmail.com>
> *Sent:* Tuesday, September 13, 2022 9:01 AM
> *To:* freesurfer@nmr.mgh.harvard.edu 
> *Subject:* [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not
> found
>
>
> External Email - Use Caution
>
> To whom it may concern,
>
>
>
> Apologies for my first post, I was a little bit confounded as to how I can
> reach for help.
>
> I would like to use the segmentation of hippocampal subfields and the
> nuclei of the amygdala.
> Currently, I am working with Ubuntu on windows with Freesurfer 7.3.2.
>
>
> I am trying to install MATLAB Runtime 2019b to run the command
> segmentHA_T1.sh for the segmentation as described above. The following
> command shows the corresponding error:
>
>
>
> ylee6@LAPTOP-63HA9ANS: /usr/local/freesurfer/7.3.2/bin$ fs_install_mcr
> R2019b
>
>   % Total% Received % Xferd  Average Speed   TimeTime Time
> Current
>
>  Dload  Upload   Total   SpentLeft
> Speed
>
> 100 2657M  100 2657M0 0  10.0M  0  0:04:25  0:04:25 --:--:--
> 10.1M
>

Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

[Wighton, Paul]

Hi Justina,

Ok so it looks like the install script is getting further and has extracted the 
matlab runtime environment into a temporary directory 
(/tmp/tmp.nGZQXYOgR8/install-target/v97) but during the final step, it is 
trying to move that temporary directory to a location inside the FreeSurfer 
directory (/usr/local/freesurfer/7.3.2/MCRv97) and it is once again running 
into a 'Permission Denied' error.

Can you try re-installing the matlab runtime by running `sudo fs_install_mcr 
R2019b` so that the install script has permissions to write to the FreeSurfer 
directory?

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Justina Lee 

Sent: Tuesday, September 13, 2022 1:58 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

Thank you Paul for your help!

This seems to have solved the issue, as I can now run the command 
fs_install_mcr R2019b. It has ended successfully with this end message stated 
below:



mv: cannot move '/tmp/tmp.nGZQXYOgR8/install-target/v97' to 
'/usr/local/freesurfer/7.3.2/MCRv97': Permission denied



I think this problem persists with my next issue, which is using the command 
segmentHA_T1.sh. When I try to run this command again it gives me the following 
error:



ERROR: cannot find Matlab 2019b runtime in location:



/usr/local/freesurfer/7.3.2/MCRv97



It is looking for either:

  bin/glnxa64/libmwlaunchermain.so(Linux 64b) or

  bin/maci64/libmwlaunchermain.dylib (Mac 64b)



The hippocampal/amygdala and brainstem modules require the (free) Matlab 
runtime.

You will need to download the Matlab Compiler Runtime (MCR) for Matlab 2019b.

To do so, please run the following command (you might need root permissions):



fs_install_mcr R2019b



I have seen that the pathway for fs_install_mcr is located in the 
usr/local/freesurfer/7.3.2 instead of in the location stated in the error 
above. When I try to search this location there is no such existing directory. 
This can be the same for bin/glnxa64/libmwlaunchermain.so.



Do I need to create a new file for where the runtime should be stored? Or 
create a file for the bin/glnxa64/libmwlaunchermain.so to be stored? Should the 
fs_installl_mcr R2019b be stored under bin for this command to work?

Hope you can continue to help me with my follow-up issue, I appreciate it a lot.

Thank you so much.



Sincerely,
Justina

On Tue, Sep 13, 2022 at 4:35 PM Wighton, Paul 
mailto:pwigh...@mgh.harvard.edu>> wrote:
Hi Justina,

It looks like the matlab installer is trying to use unzip but it can't find it.

Can you try running:
`sudo apt-get install unzip`

To install unzip then try the matlab installer again?

-Paul

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of You Na Lee mailto:justinale...@gmail.com>>
Sent: Tuesday, September 13, 2022 9:01 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

To whom it may concern,



Apologies for my first post, I was a little bit confounded as to how I can 
reach for help.


I would like to use the segmentation of hippocampal subfields and the nuclei of 
the amygdala.
Currently, I am working with Ubuntu on windows with Freesurfer 7.3.2.

I am trying to install MATLAB Runtime 2019b to run the command segmentHA_T1.sh 
for the segmentation as described above. The following command shows the 
corresponding error:



ylee6@LAPTOP-63HA9ANS: /usr/local/freesurfer/7.3.2/bin$ fs_install_mcr R2019b

  % Total% Received % Xferd  Average Speed   TimeTime Time  Current

 Dload  Upload   Total   SpentLeft  Speed

100 2657M  100 2657M0 0  10.0M  0  0:04:25  0:04:25 --:--:-- 10.1M

/usr/local/freesurfer/7.3.2/bin/fs_install_mcr: line 62: unzip: command not 
found



I am currently struggling to find the solution to this issue. Is the 
installation not in the correct path? Is MATLAB Runtime installed at all? 
Should an already existing matlab file be deleted?
Any help would be much appreciated.



Sincerely,

Justina







Sent from 
Mail<https://secure-web.cisco.com/1JF-rDYMVgKJTrVPsWHUacVbsZGxWoxGE8qofNJGanBLzB5H4xG_TSIyr-kKCyfB-OL5ahOLtropBWGT0WNStX9nlY96XmLI4PEcLyxRbpYACqwCkjWGnJ97rPRssexnOq1RJRlrOg_69B_HLSu5yX5bgMIHOh0IfF9pQcTT3TVu3DK8hZxWZSK0gfICgCNrQacXt91cfezI3FeQnjTGxoKqOqzHBsXJaNuI8JxuVMfCrweNj79o9pN5_cVgjrPSCSa5uR_IxkKANQ87K9laDUXpbpf1YpKyxu3k05hdqJLTPSgkt-wfEOgojaS7t3BsJWoxyJ2fHAPhk2SP958H0aA/https%3A%2F%2Fgo.microsoft.com%2Ffwlink%2F%3FLinkId%3D550986>
 for Windows



___
Freesurfer m

Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

[Justina Lee]

External Email - Use Caution

Thank you Paul for your help!


This seems to have solved the issue, as I can now run the command
fs_install_mcr R2019b. It has ended successfully with this end message
stated below:



mv: cannot move '/tmp/tmp.nGZQXYOgR8/install-target/v97' to
'/usr/local/freesurfer/7.3.2/MCRv97': Permission denied



I think this problem persists with my next issue, which is using the
command segmentHA_T1.sh. When I try to run this command again it gives me
the following error:



ERROR: cannot find Matlab 2019b runtime in location:



/usr/local/freesurfer/7.3.2/MCRv97



It is looking for either:

  bin/glnxa64/libmwlaunchermain.so(Linux 64b) or

  bin/maci64/libmwlaunchermain.dylib (Mac 64b)



The hippocampal/amygdala and brainstem modules require the (free) Matlab
runtime.

You will need to download the Matlab Compiler Runtime (MCR) for Matlab
2019b.

To do so, please run the following command (you might need root
permissions):



fs_install_mcr R2019b



I have seen that the pathway for fs_install_mcr is located in the
usr/local/freesurfer/7.3.2 instead of in the location stated in the error
above. When I try to search this location there is no such existing
directory. This can be the same for bin/glnxa64/libmwlaunchermain.so.



Do I need to create a new file for where the runtime should be stored? Or
create a file for the bin/glnxa64/libmwlaunchermain.so to be stored? Should
the fs_installl_mcr R2019b be stored under bin for this command to work?

Hope you can continue to help me with my follow-up issue, I appreciate it a
lot.

Thank you so much.



Sincerely,
Justina

On Tue, Sep 13, 2022 at 4:35 PM Wighton, Paul 
wrote:

> Hi Justina,
>
> It looks like the matlab installer is trying to use unzip but it can't
> find it.
>
> Can you try running:
> `sudo apt-get install unzip`
>
> To install unzip then try the matlab installer again?
>
> -Paul
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of You Na Lee <
> justinale...@gmail.com>
> *Sent:* Tuesday, September 13, 2022 9:01 AM
> *To:* freesurfer@nmr.mgh.harvard.edu 
> *Subject:* [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not
> found
>
>
> External Email - Use Caution
>
> To whom it may concern,
>
>
>
> Apologies for my first post, I was a little bit confounded as to how I can
> reach for help.
>
> I would like to use the segmentation of hippocampal subfields and the
> nuclei of the amygdala.
> Currently, I am working with Ubuntu on windows with Freesurfer 7.3.2.
>
>
> I am trying to install MATLAB Runtime 2019b to run the command
> segmentHA_T1.sh for the segmentation as described above. The following
> command shows the corresponding error:
>
>
>
> ylee6@LAPTOP-63HA9ANS: /usr/local/freesurfer/7.3.2/bin$ fs_install_mcr
> R2019b
>
>   % Total% Received % Xferd  Average Speed   TimeTime Time
> Current
>
>  Dload  Upload   Total   SpentLeft
> Speed
>
> 100 2657M  100 2657M0 0  10.0M  0  0:04:25  0:04:25 --:--:--
> 10.1M
>
> /usr/local/freesurfer/7.3.2/bin/fs_install_mcr: line 62: unzip: command
> not found
>
>
>
> I am currently struggling to find the solution to this issue. Is the
> installation not in the correct path? Is MATLAB Runtime installed at all?
> Should an already existing matlab file be deleted?
> Any help would be much appreciated.
>
>
>
> Sincerely,
>
> Justina
>
>
>
>
>
>
>
> Sent from Mail
> 
> for Windows
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/13hztnzjV4NG8MRS_WPAvkQDaoH3MtDTzQGVDegG1V9tB3vNAeQxThejPX_wGtCRjJ3QWFM_JqnS5VBaOktcLzveKxjIX3MA5p2FjSdBZCoFXLtQ8Z1KyKvtTr-aGSjUmS03KRcPg02rCBvEhWmoJbDCQsf8zWfExuxR-u4fl-PYnkCrPWM9hUnmXrZd2WEFL8AmEvxNDuEdQuaMSEDPGPtvx0RN5AfCTFUb79CJ6vuveAr1iWf0-gU3NHQNZ1vKIkflLgYP8q2yBFTSLhEcUy23TWxVYYoANhKGSeUYuR2Lsdk56Uy1D8vvtTbV9Gc1XKCXLh1Ig_3pL6k_OJiakhw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
> The information in this e-mail is intended only for the person to whom it
> is addressed.  If you believe this e-mail was sent to you in error and the
> e-mail contains patient information, please contact the Mass General
> Brigham Compliance HelpLine at
> 

Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

[Wighton, Paul]

Hi Justina,

It looks like the matlab installer is trying to use unzip​ but it can't find it.

Can you try running:
`sudo apt-get install unzip`

To install unzip then try the matlab installer again?

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of You Na Lee 

Sent: Tuesday, September 13, 2022 9:01 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


External Email - Use Caution

To whom it may concern,



Apologies for my first post, I was a little bit confounded as to how I can 
reach for help.


I would like to use the segmentation of hippocampal subfields and the nuclei of 
the amygdala.
Currently, I am working with Ubuntu on windows with Freesurfer 7.3.2.

I am trying to install MATLAB Runtime 2019b to run the command segmentHA_T1.sh 
for the segmentation as described above. The following command shows the 
corresponding error:



ylee6@LAPTOP-63HA9ANS: /usr/local/freesurfer/7.3.2/bin$ fs_install_mcr R2019b

  % Total% Received % Xferd  Average Speed   TimeTime Time  Current

 Dload  Upload   Total   SpentLeft  Speed

100 2657M  100 2657M0 0  10.0M  0  0:04:25  0:04:25 --:--:-- 10.1M

/usr/local/freesurfer/7.3.2/bin/fs_install_mcr: line 62: unzip: command not 
found



I am currently struggling to find the solution to this issue. Is the 
installation not in the correct path? Is MATLAB Runtime installed at all? 
Should an already existing matlab file be deleted?
Any help would be much appreciated.



Sincerely,

Justina







Sent from 
Mail
 for Windows


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
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